Replace MV2_ENABLE_AFFINITY=0 with MV2_CPU_BINDING_POLICY=hybrid.

OSC's Ascend cluster was installed in fall 2022 and is a Dell-built, AMD EPYC™ CPUs with NVIDIA A100 80GB GPUs cluster devoted entirely to intensive GPU processing. 

Hardware

Detailed system specifications:

• 24 Power Edge XE 8545 nodes, each with:
  • 2 AMD EPYC 7643 (Milan) processors (2.3 GHz, each with 44 usable cores) 
  • 4 NVIDIA A100 GPUs with 80GB memory each, supercharged by NVIDIA NVLink
  • 921GB usable RAM
  • 12.8TB NVMe internal storage​
• 2,112 total usable cores
  • 88 cores/node & 921GB of memory/node
• Mellanox/NVIDA 200 Gbps HDR InfiniBand​
• Theoretical system peak performance
  • 1.95 petaflops
• 2 login nodes
  •  IP address: 192.148.247.[180-181]

How to Connect

• SSH Method

To login to Ascend at OSC, ssh to the following hostname:

ascend.osc.edu 

You can either use an ssh client application or execute ssh on the command line in a terminal window as follows:

ssh <username>@ascend.osc.edu

You may see a warning message including SSH key fingerprint. Verify that the fingerprint in the message matches one of the SSH key fingerprints listed here, then type yes.

From there, you are connected to the Ascend login node and have access to the compilers and other software development tools. You can run programs interactively or through batch requests. We use control groups on login nodes to keep the login nodes stable. Please use batch jobs for any compute-intensive or memory-intensive work. See the following sections for details.

• OnDemand Method

You can also login to Ascend at OSC with our OnDemand tool. The first step is to log into OnDemand. Then once logged in you can access Ascend by clicking on "Clusters", and then selecting ">_Ascend Shell Access".

Instructions on how to connect to OnDemand can be found at the OnDemand documentation page.

File Systems

Ascend accesses the same OSC mass storage environment as our other clusters. Therefore, users have the same home directory as on the old clusters. Full details of the storage environment are available in our storage environment guide.

Software Environment

The module system on Ascend is the same as on the Owens and Pitzer systems. Use  module load <package>  to add a software package to your environment. Use  module list  to see what modules are currently loaded and  module avail  to see the modules that are available to load. To search for modules that may not be visible due to dependencies or conflicts, use  module spider . 

You can keep up to the software packages that have been made available on Ascend by viewing the Software by System page and selecting the Ascend system.

Batch Specifics

Refer to this Slurm migration page to understand how to use Slurm on the Ascend cluster.  

Using OSC Resources

For more information about how to use OSC resources, please see our guide on batch processing at OSC. For specific information about modules and file storage, please see the Batch Execution Environment page.

OSC's Owens cluster being installed in 2016 is a Dell-built, Intel® Xeon® processor-based supercomputer.

,

Hardware

Detailed system specifications:

• 824 Dell Nodes
• Dense Compute

  • 648 compute nodes (Dell PowerEdge C6320 two-socket servers with Intel Xeon E5-2680 v4 (Broadwell, 14 cores, 2.40GHz) processors, 128GB memory)

• GPU Compute

  • 160 ‘GPU ready’ compute nodes -- Dell PowerEdge R730 two-socket servers with Intel Xeon E5-2680 v4 (Broadwell, 14 cores, 2.40GHz) processors, 128GB memory

  • NVIDIA Tesla P100 (Pascal) GPUs -- 5.3TF peak (double precision), 16GB memory

• Analytics

  • 16 huge memory nodes (Dell PowerEdge R930 four-socket server with Intel Xeon E5-4830 v3 (Haswell 12 core, 2.10GHz) processors, 1,536GB memory, 12 x 2TB drives)

• 23,392 total cores
  • 28 cores/node  & 128GB of memory/node
• Mellanox EDR (100Gbps) Infiniband networking

• Theoretical system peak performance
  • ~750 teraflops (CPU only)
• 4 login nodes:
  • Intel Xeon E5-2680 (Broadwell) CPUs
  • 28 cores/node and 256GB of memory/node
  • IP address: 192.148.247.[141-144]

How to Connect

• SSH Method

To login to Owens at OSC, ssh to the following hostname:

owens.osc.edu 

You can either use an ssh client application or execute ssh on the command line in a terminal window as follows:

ssh <username>@owens.osc.edu

You may see warning message including SSH key fingerprint. Verify that the fingerprint in the message matches one of the SSH key fingerprint listed here, then type yes.

From there, you are connected to Owens login node and have access to the compilers and other software development tools. You can run programs interactively or through batch requests. We use control groups on login nodes to keep the login nodes stable. Please use batch jobs for any compute-intensive or memory-intensive work. See the following sections for details.

• OnDemand Method

You can also login to Owens at OSC with our OnDemand tool. The first step is to login to OnDemand. Then once logged in you can access Owens by clicking on "Clusters", and then selecting ">_Owens Shell Access".

Instructions on how to connect to OnDemand can be found at the OnDemand documention page.

File Systems

Owens accesses the same OSC mass storage environment as our other clusters. Therefore, users have the same home directory as on the old clusters. Full details of the storage environment are available in our storage environment guide.

Software Environment

The module system is used to manage the software environment on owens. Use  module load <package>  to add a software package to your environment. Use  module list  to see what modules are currently loaded and  module avail  to see the modules that are available to load. To search for modules that may not be visible due to dependencies or conflicts, use  module spider . By default, you will have the batch scheduling software modules, the Intel compiler and an appropriate version of mvapich2 loaded.

You can keep up to on the software packages that have been made available on Owens by viewing the Software by System page and selecting the Owens system.

Compiling Code to Use Advanced Vector Extensions (AVX2)

The Haswell and Broadwell processors that make up Owens support the Advanced Vector Extensions (AVX2) instruction set, but you must set the correct compiler flags to take advantage of it. AVX2 has the potential to speed up your code by a factor of 4 or more, depending on the compiler and options you would otherwise use.

In our experience, the Intel and PGI compilers do a much better job than the gnu compilers at optimizing HPC code.

With the Intel compilers, use -xHost and -O2 or higher. With the gnu compilers, use -march=native and -O3 . The PGI compilers by default use the highest available instruction set, so no additional flags are necessary.

This advice assumes that you are building and running your code on Owens. The executables will not be portable.  Of course, any highly optimized builds, such as those employing the options above, should be thoroughly validated for correctness.

See the Owens Programming Environment page for details.

Batch Specifics

Refer to the documentation for our batch environment to understand how to use the batch system on OSC hardware. Some specifics you will need to know to create well-formed batch scripts:

• Most compute nodes on Owens have 28 cores/processors per node.  Huge-memory (analytics) nodes have 48 cores/processors per node.
• Jobs on Owens may request partial nodes.

Using OSC Resources

For more information about how to use OSC resources, please see our guide on batch processing at OSC. For specific information about modules and file storage, please see the Batch Execution Environment page.

OSC's original Pitzer cluster was installed in late 2018 and is a Dell-built, Intel® Xeon® 'Skylake' processor-based supercomputer with 260 nodes.

In September 2020, OSC installed additional 398 Intel® Xeon® 'Cascade Lake' processor-based nodes as part of a Pitzer Expansion cluster. 

Hardware

Detailed system specifications:

How to Connect

• SSH Method

To login to Pitzer at OSC, ssh to the following hostname:

pitzer.osc.edu 

You can either use an ssh client application or execute ssh on the command line in a terminal window as follows:

ssh <username>@pitzer.osc.edu

You may see a warning message including SSH key fingerprint. Verify that the fingerprint in the message matches one of the SSH key fingerprints listed here, then type yes.

From there, you are connected to the Pitzer login node and have access to the compilers and other software development tools. You can run programs interactively or through batch requests. We use control groups on login nodes to keep the login nodes stable. Please use batch jobs for any compute-intensive or memory-intensive work. See the following sections for details.

• OnDemand Method

You can also login to Pitzer at OSC with our OnDemand tool. The first step is to log into OnDemand. Then once logged in you can access Pitzer by clicking on "Clusters", and then selecting ">_Pitzer Shell Access".

Instructions on how to connect to OnDemand can be found at the OnDemand documentation page.

File Systems

Pitzer accesses the same OSC mass storage environment as our other clusters. Therefore, users have the same home directory as on the old clusters. Full details of the storage environment are available in our storage environment guide.

Software Environment

The module system on Pitzer is the same as on the Owens and Ruby systems. Use  module load <package>  to add a software package to your environment. Use  module list  to see what modules are currently loaded and  module avail  to see the modules that are available to load. To search for modules that may not be visible due to dependencies or conflicts, use  module spider . By default, you will have the batch scheduling software modules, the Intel compiler, and an appropriate version of mvapich2 loaded.

You can keep up to the software packages that have been made available on Pitzer by viewing the Software by System page and selecting the Pitzer system.

Compiling Code to Use Advanced Vector Extensions (AVX2)

The Skylake processors that make Pitzer support the Advanced Vector Extensions (AVX2) instruction set, but you must set the correct compiler flags to take advantage of it. AVX2 has the potential to speed up your code by a factor of 4 or more, depending on the compiler and options you would otherwise use.

In our experience, the Intel and PGI compilers do a much better job than the gnu compilers at optimizing HPC code.

With the Intel compilers, use -xHost and -O2 or higher. With the gnu compilers, use -march=native and -O3 . The PGI compilers by default use the highest available instruction set, so no additional flags are necessary.

This advice assumes that you are building and running your code on Pitzer. The executables will not be portable.  Of course, any highly optimized builds, such as those employing the options above, should be thoroughly validated for correctness.

See the Pitzer Programming Environment page for details.

Batch Specifics

Refer to this Slurm migration page to understand how to use Slurm on the Pitzer cluster. Some specifics you will need to know to create well-formed batch scripts:

• OSC enables PBS compatibility layer provided by Slurm such that PBS batch scripts that used to work in the previous Torque/Moab environment mostly still work in Slurm. 
• Pitzer is a heterogeneous system with mixed types of CPUs after the expansion as shown in the above table. Please be cautious when requesting resources on Pitzer and check this page for more detailed discussions
• Jobs on Pitzer may request partial nodes.  

Using OSC Resources

For more information about how to use OSC resources, please see our guide on batch processing at OSC and Slurm migration. For specific information about modules and file storage, please see the Batch Execution Environment page.

OSC offers GPU computing on all its systems.  While GPUs can provide a significant boost in performance for some applications, the computing model is very different from the CPU.  This page will discuss some of the ways you can use GPU computing at OSC.

Accessing GPU Resources

#SBATCH --gpus-per-node=1

srun --gpu_cmode=exclusive

srun --gpu_cmode=shared

Using GPU-enabled Applications

Libraries with GPU Support

Direct GPU Programming

About OSC GPU Hardware

Examples

The only access to significant resources on the HPC machines is through the batch process.

Why use a batch system?

Access to the OSC clusters is through a system of login nodes. These nodes are reserved solely for the purpose of managing your files and submitting jobs to the batch system. Acceptable activities include editing/creating files, uploading and downloading files of moderate size, and managing your batch jobs. You may also compile and link small-to-moderate size programs on the login nodes.

CPU time and memory usage are severely limited on the login nodes. There are typically many users on the login nodes at one time. Extensive calculations would degrade the responsiveness of those nodes.

The batch system allows users to submit jobs requesting the resources (nodes, processors, memory, GPUs) that they need. The jobs are queued and then run as resources become available. The scheduling policies in place on the system are an attempt to balance the desire for short queue waits against the need for efficient system utilization.

Interactive vs. batch

When you type commands in a login shell and see a response displayed, you are working interactively. To run a batch job, you put the commands into a text file instead of typing them at the prompt. You submit this file to the batch system, which will run it as soon as resources become available. The output you would normally see on your display goes into a log file. You can check the status of your job interactively and/or receive emails when it begins and ends execution.

Terminology

The batch system used at OSC is SLURM. A central manager slurmctld, monitors resources and work. You’ll need to understand the terms cluster, node,  and processor (core) in order to request resources for your job. See HPC basics if you need this background information.

The words “parallel” and “serial” as used by SLURM can be a little misleading. From the point of view of the batch system a serial job is one that uses just one node, regardless of how many processors it uses on that node. Similarly, a parallel job is one that uses more than one node. More standard terminology considers a job to be parallel if it involves multiple processes.

Batch processing overview

Here is a very brief overview of how to use the batch system.

Choose a cluster

Before you start preparing a job script you should decide which cluster you want your job to run on, Owens or Pitzer. This decision will probably be based on the resources available on each system. Remember which cluster you’re using because the batch systems are independent.

Prepare a job script

Your job script is a text file that includes SLURM directives as well as the commands you want executed. The directives tell the batch system what resources you need, among other things. The commands can be anything you would type at the login prompt. You can prepare the script using any editor.

Submit the job

You submit your job to the batch system using the sbatch command, with the name of the script file as the argument. The sbatch command responds with the job ID that was given to your job, typically a 6- or 7-digit number.

Wait for the job to run

Your job may wait in the queue for minutes or days before it runs, depending on system load and the resources requested. It may then run for minutes or days. You can monitor your job’s progress or just wait for an email telling you it has finished.

Retrieve your output

The log file (screen output) from your job will be in the directory you submitted the job from by default. Any other output files will be wherever your script put them.

Shell and initialization

Your batch script executes in a shell on a compute node. The environment is identical to what you get when you connect to a login node except that you have access to all the resources requested by your job. The shell that Slurm uses is determined by the first line of the job script (it is by default #!/bin/bash). The appropriate “dot-files” ( .login , .profile , .cshrc ) will be executed, the same as when you log in. (For information on overriding the default shell, see the Job Scripts section.)

The job begins in the directory that it was submitted from. You can use the cd command to change to a different directory. The environment variable $SLURM_SUBMIT_DIR makes it easy to return to the directory from which you submitted the job:

cd $SLURM_SUBMIT_DIR

Modules

There are dozens of software packages available on OSC’s systems, many of them with multiple versions. You control what software is available in your environment by loading the module for the software you need. Each module sets certain environment variables required by the software.

If you are running software that was installed by OSC, you should check the software documentation page to find out what modules to load.

Several modules are automatically loaded for you when you login or start a batch script. These default modules include

• modules required by the batch system
• the Intel compiler suite
• an MPI package compatible with the default compiler (for parallel computing)

The module command has a number of subcommands. For more details, type module help.

Certain modules are incompatible with each other and should never be loaded at the same time. Examples are different versions of the same software or multiple installations of a library built with different compilers.

Note to those who build or install their own software: Be sure to load the same modules when you run your software that you had loaded when you built it, including the compiler module.

Each module has both a name and a version number. When more than one version is available for the same name, one of them is designated as the default. For example, the following modules are available for the Intel compilers on Owens: (Note: The versions shown might be out of date but the concept is the same.)

• intel/12.1.0 (default)
• intel/12.1.4.319

If you specify just the name, it refers to the default version or the currently loaded version, depending on the context. If you want a different version, you must give the entire string including the version information.

You can have only one compiler module loaded at a time, either intel, pgi, or gnu. The intel module is loaded initially; to change to pgi or gnu, do a module swap (see example below).

Some software libraries have multiple installations built for use with different compilers. The module system will load the one compatible with the compiler you have loaded. If you swap compilers, all the compiler-dependent modules will also be swapped.

Special note to gnu compiler users: While the gnu compilers are always in your path, you should load the gnu compiler module to ensure you are linking to the correct library versions.

To list the modules you have loaded:

module list

To see all modules that are compatible with your currently loaded modules:

module avail

To see all modules whose names start with fftw:

module avail fftw

To see all possible modules:

module spider

To see all possible modules whose names start with fftw:

module spider fftw

To load the fftw3 module that is compatible with your current compiler:

module load fftw3

To unload the fftw3 module:

module unload fftw3

To load the default version of the abaqus module (not compiler-dependent):

module load abaqus

To load a different version of the abaqus module:

module load abaqus/6.8-4

To unload whatever abaqus module you have loaded:

module unload abaqus

To swap the intel compilers for the pgi compilers (unloads intel, loads pgi):

module swap intel pgi

To swap the default version of the intel compilers for a different version:

module swap intel intel/12.1.4.319

To display help information for the mkl module:

module help mkl

To display the commands run by the mkl module:

module show mkl

To use a locally installed module, first import the module directory:

module use [/path/to/modulefiles]

And then load the module:

module load localmodule

SLURM environment variables

Your batch execution environment has all the environment variables that your login environment has plus several that are set by the batch system. This section gives examples for using some of them. For more information see man sbatch.

Directories

Several directories may be useful in your job.

The absolute path of the directory your job was submitted from is $SLURM_SUBMIT_DIR.

Each job has a temporary directory, $TMPDIR , on the local disk of each node assigned to it. Access to this directory is much faster than access to your home or project directory. The files in this directory are not visible from all the nodes in a parallel job; each node has its own directory. The batch system creates this directory when your job starts and deletes it when your job ends. To copy file input.dat to $TMPDIR on your job’s first node:

cp input.dat $TMPDIR

For parallel job, to copy file input.dat to $TMPDIR on all your job’s nodes:

sbcast input.dat $TMPDIR/input.dat

Each job also has a temporary directory, $PFSDIR , on the parallel scratch file system, if users add node attribute "pfsdir" in the batch request (--gres=pfsdir). This is a single directory shared by all the nodes a job is running on. Access is faster than access to your home or project directory but not as fast as $TMPDIR . The batch system creates this directory when your job starts and deletes it when your job ends. To copy the file output.dat from this directory to the directory you submitted your job from:

cp $PFSDIR/output.dat $SLURM_SUBMIT_DIR

The $HOME environment variable refers to your home directory. It is not set by the batch system but is useful in some job scripts. It is better to use $HOME than to hardcode the path to your home directory. To access a file in your home directory:

cat $HOME/myfile

Job information

A list of the nodes and cores assigned to your job is obtained using srun hostname |sort -n

For GPU jobs, a list of the GPUs assigned to your job is in the file $SLURM_GPUS_ON_NODE. To display this file:

cat $SLURM_GPUS_ON_NODE

If you use a job array, each job in the array gets its identifier within the array in the variable $SLURM_ARRAY_JOB_ID. To pass a file name parameterized by the array ID into your application:

./a.out input_$SLURM_ARRAY_JOB_ID.dat

To display the numeric job identifier assigned by the batch system:

echo $SLURM_JOB_ID

To display the job name:

echo $SLURM_JOB_NAME

Use fast storage

If your job does a lot of file-based input and output, your choice of file system can make a huge difference in the performance of the job.

Shared file systems

Your home directory is located on shared file systems, providing long-term storage that is accessible from all OSC systems. Shared file systems are relatively slow. They cannot handle heavy loads such as those generated by large parallel jobs or many simultaneous serial jobs. You should minimize the I/O your jobs do on the shared file systems. It is usually best to copy your input data to fast temporary storage, run your program there, and copy your results back to your home directory.

Batch-managed directories

Batch-managed directories are temporary directories that exist only for the duration of a job. They exist on two types of storage: disks local to the compute nodes and a parallel scratch file system.

A big advantage of batch-managed directories is that the batch system deletes them when a job ends, preventing clutter on the disk.

A disadvantage of batch-managed directories is that you can’t access them after your job ends. Be sure to include commands in your script to copy any files you need to long-term storage. To avoid losing your files if your job ends abnormally, for example by hitting its walltime limit, include a trap command in your script (Note:  trap  commands do not work in csh and tcsh shell batch scripts). The following example creates a subdirectory in $SLURM_SUBMIT_DIR and copies everything from $TMPDIR into it in case of abnormal termination.

trap "cd $SLURM_SUBMIT_DIR;mkdir $SLURM_JOB_ID;cp -R $TMPDIR/* $SLURM_SUBMIT_DIR;exit" TERM

If a node your job is running on crashes, the trap command may not be executed. It may be possible to recover your batch-managed directories in this case. Contact OSC Help for assistance.  For other details on retrieving files from unexpectedly terminated jobs see this FAQ.

Local disk space

The fastest storage is on a disk local to the node your job is running on, accessed through the environment variable $TMPDIR . The main drawback to local storage is that each node of a parallel job has its own directory and cannot access the files on other nodes. 

Local disk space should be used only through the batch-managed directory created for your job. Please do not use /tmp directly because your files won’t be cleaned up properly.

Parallel file system

The parallel file system including project directory and scratch directory is faster than the shared file systems for large-scale I/O and can handle a much higher load. It is efficient for reading and writing data in large blocks, and should not be used for I/O involving many small accesses.

The scratch file system can be used through the batch-managed directory created for your job. The path for this directory is in the environment variable $PFSDIR . You should use it when your files must be accessible by all the nodes in your job and also when your files are too large for the local disk.

You may also create a directory for yourself in scratch file system and use it the way you would use any other directory. This directory will not be backed up; files are subject to deletion after some number of months.

Note: You should not copy your executable files to $PFSDIR. They should be run from your home directories or from $TMPDIR.

A job script is a text file containing job setup information for the batch system followed by commands to be executed. It can be created using any text editor and may be given any name. Some people like to name their scripts something like myscript.job or myscript.sh, but myscript works just as well.

A job script is simply a shell script. It consists of SLURM directives, comments, and executable statements. The # character indicates a comment, although lines beginning with #SBATCH are interpreted as SLURM directives. Blank lines can be included for readability.

Contents

1. SBATCH header lines
2. Resource limits
3. Executable section
4. Considerations for parallel jobs
   • Scripts issues in parallel jobs
   • Run parallel jobs with srun 
   • File transmission on all nodes
5. Batch script examples

SBATCH header lines

A job script must start with a shabang #!  (#!/bin/bash is commonly used but you can choose others) following by several lines starting with #SBATCH. These are SLURM SBATCH directives or header lines. They provide job setup information used by SLURM, including resource requests, email options, and more. The header lines may appear in any order, but they must precede any executable lines in your script. Alternatively, you may provide these directives (without the #SBATCH notation) on the command line with the sbatch command.

$ sbatch --jobname=test_job myscript.sh

Resource limits

Options used to request resources, including nodes, memory, time, and software flags, as described below.

Walltime

The walltime limit is the maximum time your job will be allowed to run, given in seconds or hours:minutes:seconds. This is elapsed time. If your job exceeds the requested time, the batch system will kill it. If your job ends early, you will be charged only for the time used.

The default value for walltime is 1:00:00 (one hour).

To request 20 hours of wall clock time:

#SBATCH --time=20:00:00

It is important to carefully estimate the time your job will take. An underestimate will lead to your job being killed. A large overestimate may prevent your job from being backfilled or fitting into an empty time slot.

Tasks (cores), nodes and GPUs

The tasks and nodes resource limits specify not just the number of nodes but also the properties of those nodes. The properties differ between clusters but may include the number of cores per node, the number of GPUs per node (gpus), and the type of node.

Serial job

To request one CPU core (sequential job):

#SBATCH --ntasks=1

This is the default if you don't specify any tasks and nodes resource limit.

To request 6 CPU cores on the same node:

#SBATCH --ntasks=6

Parallel job

To request 4 nodes:

#SBATCH --nodes=4

In some practices, you may want to request 4 nodes with 10 CPU cores per node:

#SBATCH --nodes=4 --ntasks-per-node=10

However, under our current scheduling policy a parallel job (which uses more than one node) is always given full nodes. You can easily use just part of each node even if the entire nodes are allocated (see the section srun in parallel jobs).

Computing nodes on Pitzer cluster have 40 or 48 cores per node. The job can be constrained on 40-core (or 48-core) nodes only by using  --constraint:

#SBATCH --constraint=40core

GPU job

To request 2 nodes with 2 GPUs (2-GPU nodes are only available on Pitzer)

#SBATCH --nodes=2
#SBATCH --gpus-per-node=2

To request one node with use of 6 CPU cores and 1 GPU:

#SBATCH --ntasks=6
#SBATCH --gpus-per-node=1

Memory

The memory limit is the total amount of memory needed across all nodes. There is no need to specify a memory limit unless you need a large-memory node or your memory requirements are disproportionate to the number of cores you are requesting. For parallel jobs you must multiply the memory needed per node by the number of nodes to get the correct limit; you should usually request whole nodes and omit the memory limit.

Default units are bytes, but values are usually expressed in megabytes (mem=4000MB) or gigabytes (mem=4GB).

To request 4GB memory (see note below):

#SBATCH --mem=4gb

or

#SBATCH --mem=4000mb

To request 24GB memory:

#SBATCH --mem=24000mb

Note: The amount of memory available per node is slightly less than the nominal amount. If you want to request a fraction of the memory on a node, we recommend you give the amount in MB, not GB; 24000MB is less than 24GB. (Powers of 2 vs. powers of 10 -- ask a computer science major.)

Software licenses

If you are using a software package with a limited number of licenses, you should include the license requirement in your script. See the OSC documentation for the specific software package for details.

Example requesting five abaqus licenses:

#SBATCH --licenses=abaqus@osc:5

Job name

You can optionally give your job a meaningful name. The default is the name of the batch script, or just "sbatch" if the script is read on sbatch's standard input. The job name is used as part of the name of the job log files; it also appears in lists of queued and running jobs. The name may be up to 15 characters in length, no spaces are allowed, and the first character must be alphabetic.

Example:

#SBATCH --job-name=my_first_job

Mail options

You may choose to receive email when your job begins, when it ends, and/or when it fails. The email will be sent to the address we have on record for you. You should use only one --mail-type=<type> directive and include all the options you want.

To receive an email when your job begins, ends or fails:

#SBATCH --mail-type=BEGIN,END,FAIL

To receive an email for all types:

#SBATCH --mail-type=ALL

The default email recipient is the submitting user, but you can include other users or email addresses:

#SBATCH --mail-user=osu1234,osu4321,username@osu.edu

Job log files

By default, SLURM directs both standard output and standard error to one log file. For job 123456, the log file will be named slurm-123456.out. You can specify name for the log file.

#SBATCH --output=myjob.out.%j

 where the %j is replaced by the job ID.

Identify Project

Job scripts are required to specify a project account.

Get a list of current projects by using the OSCfinger command and looking in the SLURM accounts section:

OSCfinger userex
Login: userex                                     Name: User Example
Directory: /users/PAS1234/userex (CREATED)        Shell: /bin/bash
E-mail: user-ex@osc.edu
Contact Type: REGULAR
Primary Group: pas1234
Groups: pas1234,pas4321
Institution: Ohio Supercomputer Center
Password Changed: Dec 11 2020 21:05               Password Expires: Jan 12 2021 01:05 AM
Login Disabled: FALSE                             Password Expired: FALSE
SLURM Enabled: TRUE
SLURM Clusters: owens,pitzer
SLURM Accounts: pas1234,pas4321 <<===== Look at me !!
SLURM Default Account: pas1234
Current Logins:

To specify an account use:

#SBATCH --account=PAS4321

For more details on errors you may see when submitting a job, see messages from sbatch.

Executable section

The executable section of your script comes after the header lines. The content of this section depends entirely on what you want your job to do. We mention just two commands that you might find useful in some circumstances. They should be placed at the top of the executable section if you use them.

Command logging

The set -x command (set echo in csh) is useful for debugging your script. It causes each command in the batch file to be printed to the log file as it is executed, with a + in front of it. Without this command, only the actual display output appears in the log file.

To echo commands in bash or ksh:

set -x

To echo commands in tcsh or csh:

set echo on

Signal handling

Signals to gracefully and then immediately kill a job will be sent for various circumstances, for example if it runs out of wall time or is killed due to out-of-memory. In both cases, the job may stop before all the commands in the job script can be executed.

The sbatch flag --signal can be used to specify commands to be ran when these signals are received by the job.

Below is an example:

#!/bin/bash
#SBATCH --job-name=minimal_trap
#SBATCH --time=2:00
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --output=%x.%A.log
#SBATCH --signal=B:USR1@60

function my_handler() {
  echo "Catching signal"
  touch $SLURM_SUBMIT_DIR/job_${SLURM_JOB_ID}_caught_signal
  cd $SLURM_SUBMIT_DIR
  mkdir $SLURM_JOB_ID
  cp -R $TMPDIR/* $SLURM_JOB_ID
  exit
}

trap my_handler USR1
trap my_handler TERM

my_process &
wait

It is typically used to copy output files from a temporary directory to a home or project directory. The following example creates a directory in   $SLURM_SUBMIT_DIR  and copies everything from $TMPDIR into it. This executes only  if the job terminates abnormally. In some cases, even with signal handling, the job still may not be able to execute the handler.

For other details on retrieving files from unexpectedly terminated jobs see this FAQ.

Considerations for parallel jobs

Each processor on our system is fast, but the real power of supercomputing comes from putting multiple processors to work on a task. This section addresses issues related to multithreading and parallel processing as they affect your batch script. For a more general discussion of parallel computing see another document.

Multithreading involves a single process, or program, that uses multiple threads to take advantage of multiple cores on a single node. The most common approach to multithreading on HPC systems is OpenMP. The threads of a process share a single memory space.

The more general form of parallel processing involves multiple processes, usually copies of the same program, which may run on a single node or on multiple nodes. These processes have separate memory spaces. When they need to communicate or share data, these processes typically use the Message-Passing Interface (MPI).

A program may use multiple levels of parallelism, employing MPI to communicate between nodes and OpenMP to utilize multiple processors on each node.

For more details on building and running MPI/OpenMP software, see the programing environment pages for Pitzer cluster and Owens cluster.

Script issues in parallel jobs

In a parallel job your script executes on just the first node assigned to the job, so it’s important to understand how to make your job execute properly in a parallel environment. These notes apply to jobs running on multiple nodes.

You can think of the commands (executable lines) in your script as falling into four categories.

• Commands that affect only the shell environment. These include such things as cd, module, and export (or setenv). You don’t have to worry about these. The commands are executed on just the first node, but the batch system takes care of transferring the environment to the other nodes.
• Commands that you want to have execute on only one node. These might include date or echo. (Do you really want to see the date printed 20 times in a 20-node job?) They might also include cp if your parallel program expects files to be available only on the first node. You don’t have to do anything special for these commands.
• Commands that have parallel execution, including knowledge of the batch system, built in. These include sbcast (parallel file copy) and some application software installed by OSC. You should consult the software documentation for correct parallel usage of application software.
• Any other command or program that you want to have execute in parallel must be run using srun. Otherwise, it will run on only one node, while the other nodes assigned to the job will remain idle. See examples below.

srun

The srun command runs a parallel job on cluster managed by SLURM. It is highly recommended to use srun while you run a parallel job with MPI libraries installed at OSC, including MVAPICH2, Intel MPI and OpenMPI.

The srun command has the form:

srun [srun-options] progname [prog-args]

where srun-options is a list of options to srun, progname is the program you want to run, and prog-args is a list of arguments to the program. Note that if the program is not in your path or not in your current working directory, you must specify the path as part of the name. 

By default, srun runs as many copies of progname as there are tasks (cores) assigned to the job. For example, if your job requested --ntasks=8, the following command would run 8 a.out processes:

 srun a.out

While --nodes=4 is specified, the number of tasks (ntasks) is set to nodes x CPUs on node.

The example above can be modified to pass arguments to a.out. The following example shows two arguments:

 srun a.out abc.dat 123

If the program is multithreaded, or if it uses a lot of memory, it may be desirable to run just one or less processes per node. You can specify --ntasks (or -n) along with --ntasks-per-node to do this. By modifying the above example with --nodes=4, the following example would run 8 copies of a.out, two on each node:

 srun --ntasks=8 --ntasks-per-node=2 a.out abc.dat 123

If this is a single-node job, you can skip --ntasks-per-node.

System commands can also be run with srun. The following commands create a directory named data in the $TMPDIR directory on each node:

cd $TMPDIR
srun -n $SLURM_JOB_NUM_NODES --ntasks-per-node=1 mkdir data

sbcast and sgather

If you use $TMPDIR in a parallel job, you probably want to copy files to or from all the nodes. The sbcast and sgather commands are used for this task. 

To copy one file into the directory $TMPDIR on all nodes allocated to your job:

sbcast myprog $TMPDIR/myprog

To copy one file from the directory $TMPDIR on all nodes allocated to your job: 

sgather -k $TMPDIR/mydata all_data

where the option -k will keep the file on the node, and all_data is the name of the file to be created with an appendix of source node name, meaning that you will see files all_data.node1_name, all_data.node2_name and more in the current working directory.

To recursively copy a directory from all nodes to the directory where the job is submitted:

sgather -k -r $TMPDIR $SLURM_SUBMIT_DIR/mydata

where mydata is the name of the directory to be created with an appendix of source node name. 

Environment variables for MPI

If your program combines MPI and OpenMP (or another multithreading technique), you should disable processor affinity by setting the environment variable MV2_ENABLE_AFFINITY to 0 in your script. If you don’t disable affinity, all your threads will run on the same core, negating any benefit from multithreading.

To set the environment variable in bash, include this line in your script:

export MV2_ENABLE_AFFINITY=0

To set the environment variable in csh, include this line in your script:

setenv MV2_ENABLE_AFFINITY 0

Environment variables for OpenMP

The number of threads used by an OpenMP program is typically controlled by the environment variable $OMP_NUM_THREADS. If this variable isn't set, the number of threads defaults to the number of cores you requested per node, although it can be overridden by the program.

If your job runs just one process per node and is the only job running on the node, the default behavior is what you want. Otherwise, you should set $OMP_NUM_THREADS to a value that ensures that the total number of threads for all your processes on the node does not exceed the ppn value your job requested.

For example, to set the environment variable to a value of 40 in bash, include this line in your script:

export OMP_NUM_THREADS=40

For example, to set the environment variable to a value of 40 in csh, include this line in your script:

setenv OMP_NUM_THREADS 40

Note: Some programs ignore $OMP_NUM_THREADS and determine the number of threads programmatically.

Batch script examples

Simple sequential job

The following is an example of a single-task sequential job that uses $TMPDIR as its working area. It assumes that the program mysci has already been built. The script copies its input file from the directory into $TMPDIR, runs the code in $TMPDIR, and copies the output files back to the original directory.

#!/bin/bash
#SBATCH --account=pas1234
#SBATCH --job-name=myscience
#SBATCH --time=40:00:00
#SBATCH --ntasks=1

cp mysci.in $TMPDIR
cd $TMPDIR    
/usr/bin/time ./mysci > mysci.hist
cp mysci.hist mysci.out $SLURM_SUBMIT_DIR

Serial job with OpenMP

The following example runs a multi-threaded program with 8 cores:

#!/bin/bash
#SBATCH --account=pas1234
#SBATCH --job-name=my_job
#SBATCH --time=1:00:00
#SBATCH --ntasks=8

cp a.out $TMPDIR
cd $TMPDIR
export OMP_NUM_THREADS=8
./a.out > my_results
cp my_results $SLURM_SUBMIT_DIR

Simple parallel job

Here is an example of a parallel job that uses 4 nodes, running one process per core. To illustrate the module command, this example assumes a.out was built with the GNU compiler. The module swap command is necessary when running MPI programs built with a compiler other than Intel.

#!/bin/bash
#SBATCH --account=pas1234
#SBATCH --job-name=my_job
#SBATCH --time=10:00:00
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=28

module swap intel gnu
sbcast a.out $TMPDIR/a.out
cd $TMPDIR
srun a.out
sgather -k -r $TMPDIR $SLURM_SUBMIT_DIR/my_mpi_output

Parallel job with MPI and OpenMP

This example is a hybrid (MPI + OpenMP) job. It runs one MPI process per node with X threads per process, where X must be less than or equal to physical cores per node (see the note below). The assumption here is that the code was written to support multilevel parallelism. The executable is named hybrid-program.

#!/bin/bash
#SBATCH --account=pas1234
#SBATCH --job-name=my_job
#SBATCH --time=20:00:00
#SBATCH --nodes=4
#SBATCH --ntasks-per-node=28

export OMP_NUM_THREADS=X
export MV2_CPU_BINDING_POLICY=hybrid
sbcast hybrid-program $TMPDIR/hybrid-program
cd $TMPDIR
srun -n 4 --ntasks-per-node=1 hybrid-program
sgather -k -r $TMPDIR $SLURM_SUBMIT_DIR/my_hybrid_output

Note that computing nodes on Pitzer cluster have 40 or 48 cores per node and computing nodes on Owens cluster have 28 cores per node. If you want X to be all physical cores per node and to be independent of clusters, use the input environment variable SLURM_CPUS_ON_NODE:

export OMP_NUM_THREADS=$SLURM_CPUS_ON_NODE

Job scripts are submitted to the batch system using the sbatch command.  Be sure to submit your job on the system you want your job to run on, or use the --cluster=<system> option to specify one.

Standard batch job

Most jobs on our system are submitted as scripts with no command-line options. If your script is in a file named myscript:

sbatch myscript

In response to this command you’ll see a line with your job ID:

Submitted batch job 123456

You’ll use this job ID (numeric part only) in monitoring your job. You can find it again using the squeue -u <username>

When you submit a job, the script is copied by the batch system. Any changes you make subsequently to the script file will not affect the job. Your input files and executables, on the other hand, are not picked up until the job starts running.

Interactive batch

The batch system supports an interactive batch mode. This mode is useful for debugging parallel programs or running a GUI program that’s too large for the login node. The resource limits (memory, CPU) for an interactive batch job are the same as the standard batch limits.

Interactive batch jobs are generally invoked without a script file.

Custom sinteractive command

OSC has developed a script to make starting an interactive session simpler.

The sinteractive command takes simple options and starts an interactive batch session automatically.  However, its behavior can be counterintuitive with respect to numbers of tasks and CPUs.  In addition, jobs launched with sinteractive can show environmental differences compared to jobs launched via other means.  As an alternative, try, e.g.:

salloc -A <proj-code> --time=500 /bin/bash

Simple serial

The example below demonstrates using sinteractive to start a serial interactive job:

sinteractive -A <proj-code>

The default if no resource options are specified is for a single core job to be submitted.

Simple parallel (single node)

To request a simple parallel job of 4 cores on a single node:

sinteractive -A <proj-code> -c 4

To setup for OpenMP executables then enter this command:

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

Parallel (multiple nodes)

To request 2 whole nodes on Pitzer with a total of 96 cores between both nodes:

sinteractive -A <proj-code> -N 2 -n 96

But note that the slurm variables SLURM_CPUS_PER_TASK, SLURM_NTASKS, and SLURM_TASKS_PER_NODE are all 1, so subsequent srun commands to launch parallel executables must explicitly specify the task and cpu numbers desired.  Unless one really needs to run in the debug queues it is in general simpler to start with an appropriate salloc command.

Using salloc and srun

An example of using salloc and srun:

salloc --account=pas1234 --x11 --nodes=2 --ntasks-per-node=28 --time=1:00:00 srun --pty /bin/bash

The salloc command requests the resources, then srun starts an interactive shell for the requested resources. Job is interactive. The --x11 flag enables X11 forwarding, which is necessary with a GUI. You will need to have a X11 server running on your computer to use X11 forwarding, see the getting connected page. The remaining flags in this example are resource requests with the same meaning as the corresponding header lines in a batch file.

After you enter this line, you’ll see something like the following:

salloc: Pending job allocation 123456
salloc: job 123456 queued and waiting for resources

Your job will be queued just like any job. When the job runs, you’ll see the following line:

salloc: job 123456 has been allocated resources
salloc: Granted job allocation 123456
salloc: Waiting for resource configuration
salloc: Nodes o0001 are ready for job

At this point, you have an interactive login shell on one of the compute nodes, which you can treat like any other login shell.

It is important to remember that OSC systems are optimized for batch processing, not interactive computing. If the system load is high, your job may wait for hours in the queue, making interactive batch impractical. Requesting a walltime limit of one hour or less is recommended because your job can run on nodes reserved for debugging.

Job arrays

If you submit many similar jobs at the same time, you should consider using a job array. With a single sbatch command, you can submit multiple jobs that will use the same script. Each job has a unique identifier, $SLURM_ARRAY_TASK_ID, which can be used to parameterize its behavior.

Individual jobs in a job array are scheduled independently, but some job management tasks can be performed on the entire array.

To submit an array of jobs numbered from 1 to 100, all using the script sim.job:

sbatch --array=1-100 sim.job

The script would use the environment variable $SLURM_ARRAY_TASK_ID, possibly as an input argument to an application or as part of a file name.

Job dependencies

It is possible to set conditions on when a job can start. The most common of these is a dependency relationship between jobs.

For example, to ensure that the job being submitted (with script sim.job) does not start until after job 123456 has finished:

sbatch --dependency=afterany:123456 sim.job

Job variables

It is possible to provide a list of environment variables that are exported to the job. 

For example, to pass the variable and its value to the job with the script sim.job, use the command:

sbatch --export=var=value​ sim.job

Many other options are available, some quite complicated; for more information, see the sbatch online manual by using the command:

man sbatch

Several commands allow you to check job status, monitor execution, collect performance statistics or even delete your job, if necessary.

Status of queued jobs

There are many possible reasons for a long queue wait — read on to learn how to check job status and for more about how job scheduling works.

squeue

Use the squeue command to check the status of your jobs, including whether your job is queued or running and information about requested resources. If the job is running, you can view elapsed time and resources used.

Here are some examples for user usr1234 and job 123456.

By itself, squeue lists all jobs in the system.

To list all the jobs belonging to a particular user:

squeue -u usr1234

To list the status of a particular job, in standard or alternate (more useful) format:

squeue -j 123456

To get more detail about a particular job:

squeue -j 123456 -l

You may also filter output by the state of a job. To view only running jobs use:

squeue -u usr1234 -t RUNNING

Other states can be seen in the JOB STATE CODES section of squeue man page using man squeue.

Additionally, JOB REASON CODES may be retrieved using the  -l with the command man squeue. These codes describe the nodes allocated to running jobs or the reasons a job is pending, which may include:

• Reason code "MaxCpuPerAccount": A user or group has reached the limit on the number of cores allowed. The rest of the user or group's jobs will be pending until the number of cores in use decreases.
• Reason code "Dependency": Dependencies among jobs or conditions that must be met before a job can run have not yet been satisfied.

You can place a hold on your own job using scontrol hold jobid. If you do not understand the state of your job, contact OSC Help for assistance.

To list blocked jobs:

squeue -u usr1234 -t PENDING

The --start option estimates the start time for a pending job. Unfortunately, these estimates are not at all accurate except for the highest priority job in the queue.

Why isn’t my job running?

There are many reasons that your job may have to wait in the queue longer than you would like, including:

• System load is high.
• A downtime has been scheduled and jobs that cannot complete by the start of that downtime are not being started. Check the system notices posted on the OSC Events page or the message of the day, displayed when you log in.
• You or your group are at the maximum processor count or running job count and your job is being held.
• Your job is requesting specialized resources, such as GPU nodes or large memory nodes or certain software licenses, that are in high demand and not available.
• Your job is requesting a lot of resources. It takes time for the resources to become available.
• Your job is requesting incompatible or nonexistent resources and can never run.
• Job is unnecessarily stuck in batch hold because of system problems (very rare).

Priority, backfill and debug reservations

Priority is a complicated function of many factors, including the processor count and walltime requested, the length of time the job has been waiting and more.

During each scheduling iteration, the scheduler will identify the highest priority job that cannot currently be run and find a time in the future to reserve for it. Once that is done, the scheduler will then try to backfill as many lower priority jobs as it can without affecting the highest priority job's start time. This keeps the overall utilization of the system high while still allowing reasonable turnaround time for high priority jobs. Short jobs and jobs requesting few resources are the easiest to backfill.

A small number of nodes are set aside during the day for jobs with a walltime limit of 1 hour or less, primarily for debugging purposes.

Observing a running job

You can monitor a running batch job as easily as you can monitor a program running interactively. Simply view the output file in read only mode to check the current output of the job.

Node status

You may check the status of a node while the job is running by visiting the OSC grafana page and using the "cluster metrics" report.

Managing your jobs

Deleting a job

Situations may arise that call for deletion of a job from the SLURM queue, such as incorrect resource limits, missing or incorrect input files or commands or a program taking too long to run (infinite loop).

The command to delete a batch job is scancel. It applies to both queued and running jobs.

Example:

scancel 123456

If you cannot delete one of your jobs, it may be because of a hardware problem or system software crash. In this case you should contact OSC Help.

Altering a queued job

You can alter certain attributes of a job in the queue using the scontrol update command. Use this command to make a change without losing your place in the queue. Please note that you cannot make any alterations to the executable portion of the script, nor can you make any changes after the job starts running.

The syntax is:

scontrol update job=<jobid> <args>

The optional arguments consist of one or more SLURM directives in the form of command-line options.

For example, to change the walltime limit on job 123456 to 5 hours and have email sent when the job ends (only):

scontrol update job=123456 timeLimit=5:00:00 mailType=End

Placing a hold on a queued job

If you want to prevent a job from running but leave it in the queue, you can place a hold on it using the scontrol hold command. The job will remain pending until you release it with the scontrol release command. A hold can be useful if you need to modify the input file for a job without losing your place in the queue.

Examples:

scontrol hold 123456
scontrol release 123456

Job statistics

Include the following commands in your batch script as appropriate to collect job statistics or performance information.

A simple way to view job information is to use this command at the end of the job:

scontrol show job=$SLURM_JOB_ID

XDMoD tool

You can use the online interactive tool XDMoD to look at usage statistics for jobs. See XDMoD overview for more information.

date

The date command prints the current date and time. It can be informative to include it at the beginning and end of the executable portion of your script as a rough measure of time spent in the job.

time

The time utility is used to measure the performance of a single command. It can be used for serial or parallel processes. Add /usr/bin/time to the beginning of a command in the batch script:

/usr/bin/time myprog arg1 arg2

The result is provided in the following format:

1. user time (CPU time spent running your program)
2. system time (CPU time spent by your program in system calls)
3. elapsed time (wallclock)
4. percent CPU used
5. memory, pagefault and swap statistics
6. I/O statistics

These results are appended to the job's error log file. Note: Use the full path “/usr/bin/time” to get all the information shown.

The batch scheduler is configured with a number of scheduling policies to keep in mind. The policies attempt to balance the competing objectives of reasonable queue wait times and efficient system utilization. The details of these policies differ slightly on each system. Exceptions to the limits can be made under certain circumstances; contact oschelp@osc.edu for details.

Hardware limits

Each system differs in the number of processors (cores) and the amount of memory and disk they have per node. We commonly find jobs waiting in the queue that cannot be run on the system where they were submitted because their resource requests exceed the limits of the available hardware. Jobs never migrate between systems, so please pay attention to these limits.

Notice in particular the large number of standard nodes and the small number of large-memory nodes. Your jobs are likely to wait in the queue much longer for a large-memory node than for a standard node. Users often inadvertently request slightly more memory than is available on a standard node and end up waiting for one of the scarce large-memory nodes, so check your requests carefully.

See cluster computing for details on the number of nodes for each type.

Walltime limits per job

Serial jobs (that is, jobs which request only one node) can run for up to 168 hours, while parallel jobs may run for up to 96 hours.

Users who can demonstrate a need for longer serial job time may request access to the longserial queue, which allows single-node jobs of up to 336 hours. Longserial access is not automatic. Factors that will be considered include how efficiently the jobs use OSC resources and whether they can be broken into smaller tasks that can be run separately.

Limits per user and group

These limits are applied separately on each system.

An individual user can have up to 128 concurrently running jobs and/or up to 2040  processor cores in use on Pitzer. All the users in a particular group/project can among them have up to 192 concurrently running jobs and/or up to 2040 processor cores in use on Pitzer. Jobs submitted in excess of these limits are queued but blocked by the scheduler until other jobs exit and free up resources.

A user may have no more than 1000 jobs submitted to both the parallel and serial job queue separately. Jobs submitted in excess of this limit will be rejected.

Priority

The priority of a job is influenced by a large number of factors, including the processor count requested, the length of time the job has been waiting, and how much other computing has been done by the user and their group over the last several days. However, having the highest priority does not necessarily mean that a job will run immediately, as there must also be enough processors and memory available to run it.

GPU Jobs

All GPU nodes are reserved for jobs that request gpus. Short non-GPU jobs are allowed to backfill on these nodes to allow for better utilization of cluster resources.

SLURM directives may appear as header lines in a batch script or as options on the sbatch command line. They specify the resource requirements of your job and various other attributes. Many of the directives are discussed in more detail elsewhere in this document. The online manual page for sbatch (man sbatch) describes many of them.

SLURM header lines must come before any executable lines in your script. Their syntax is:

#SBATCH [option]

where option can be one of the options in the table below (there are others which can be found in the manual). For example, to request 4 nodes with 40 processors per node:

#SBATCH --nodes=4
#SBTACH --ntasks-per-node=40
#SBATCH --constraint=40core

The syntax for including an option on the command line is:

sbatch [option]

For example, the following line submits the script myscript.job but adds the --time nodes directive:

sbatch --time=00:30:00 myscript.job

Slurm defaults

It is also possible to create a file which tells slurm to automatically apply certain directives to jobs.

To start, create file ~/.slurm/defaults

One option is to have the file automatically use a certain project account for job submissions. Simply add the following line to ~/.slurm/defaults

account=PEX1234

The account can also be separated by cluster.

owens:account=PEX1234
pitzer:account=PEX4321

Or even separated to only use the defaults with the sbatch command.

sbatch:*:account=PEX1234

Finally, many of the options available for the sbatch command can be set as a default. Here are some examples.

# always request two cores
ntasks-per-node=2
# on pitzer only, request a 2 hour time limit
pitzer:time=2:00:00

The batch system provides several environment variables that you may want to use in your job script. This section is a summary of the most useful of these variables. Many of them are discussed in more detail elsewhere in this document. The ones beginning with SLURM_ are described in the online manual page for sbatch (man sbatch).

The following environment variables are often used in batch scripts but are not directly related to the batch system.

This section summarizes two groups of batch-related commands: commands that are run on the login nodes to manage your jobs and commands that are run only inside a batch script. Only the most common options are described here.

Many of these commands are discussed in more detail elsewhere in this document. All have online manual pages (example: man sbatch ) unless otherwise noted.

In describing the usage of the commands we use square brackets [like this] to indicate optional arguments. The brackets are not part of the command.

Important note: The batch systems on Pitzer, Ruby, and Owens are entirely separate. Be sure to submit your jobs on a login node for the system you want them to run on. All monitoring while the job is queued or running must be done on the same system also. Your job output, of course, will be visible from both systems.

Commands for managing your jobs

These commands are typically run from a login node to manage your batch jobs. The batch systems on Pitzer and Owens are completely separate, so the commands must be run on the system where the job is to be run.

sbatch

The sbatch command is used to submit a job to the batch system.

squeue

The squeue command is used to display the status of batch jobs.

scancel

The scancel command may be used to delete a queued or running job.

slurm output file

There is an output file which stores the stdout and stderr for a running job which can be viewed to check the running job output. It is by default located in the dir where the job was submitted and has the format slurm-<jobid>.out

The output file can also be renamed and saved in any valid dir using the option --output=<filename pattern>

scontrol

The scontrol command may be used to modify the attributes of a queued (not running) job. Not all attributes can be altered.

scontrol hold/release

The qhold command allows you to place a hold on a queued job. The job will be prevented from running until you release the hold with the qrls command.

scontrol show

The scontrol show command can be used to provide details about a job that is running.

scontrol show job=$SLURM_JOB_ID

estimating start time

The squeue command can try to estimate when a queued job will start running. It is extremely unreliable, often making large errors in either direction.

squeue -j jobid \
--Format=username,jobid,account,startTime

squeue -j 123456 \ 
--Format=username,jobid,account,startTime

Commands used only inside a batch job

These commands can only be used inside a batch job.

srun

Generally used to start an mpi process during a job. Can use most of the options available also from the sbatch command.

sbcast/sgather

Tool for copying files to/from all nodes allocated in a job.

for FILE in * 
do
    sbcast -p $FILE $TMPDIR/some_directory/$FILE
done

mpiexec

Use the mpiexec command to run a parallel program or to run multiple processes simultaneously within a job. It is a replacement program for the script mpirun , which is part of the mpich package.
The OSC version of mpiexec is customized to work with our batch environment. There are other mpiexec programs in existence, but it is imperative that you use the one provided with our system.

pbsdcp

The pbsdcp command is a distributed copy command for the Slurm environment. It copies files to or from each node of the cluster assigned to your job. This is needed when copying files to directories which are not shared between nodes, such as $TMPDIR.

Options are -r for recursive and -p to preserve modification times and modes.

Note: In gather mode, if files on different nodes have the same name, they will overwrite each other. In the -g example above, the file names may have the form outfile001 , outfile002 , etc., with each node producing a different set of files.

We have licensed applications such as ansys, abaqus, and Schrodinger. These applications have a license server with a limited number of licenses, and you need to check out the licenses when you use the software each time. One problem is that the job scheduler, Slurm, doesn't communicate with the license server. As a result, a job can be launched even there are not enough licenses available, and it fails due to insufficient licenses. 

In order to prevent this happen, you need to add the software flag to your job script. The software flag will register your license requests to the Slurm license pool so that Slrum can prevent launching jobs without enough licenses available.

The syntax for software flags is

#SBATCH -L {software flag}@osc:N

where N is the requesting number of the licenses. If you need more than one software flags, you can use

#SBATCH -L {software flag1}@osc:N,{software flag2}@osc:M

For example, if you need 1 ansys and 10 ansyspar license features, then you can use

$SBATCH -L ansys@osc:1,ansyspar@osc:10

For interactive jobs, you can use, for example,

sinteractive -A {project account} -L ansys@osc:1

When you use the OnDemand VDI, Desktop, or Schrodinger apps, you can put software flags on the "Licenses" field. For OnDemand Abaqus/CAE, COMSOL Multiphysics, and Stata, the software flags will be placed automatically. And, for OnDemand Ansys Workbench, please check on "Reserve ANSYS Parallel Licenses," if you need "ansyspar" license features. 

We have the full list of software associated with software flags in the table below. For more information, please click the link on the software name.  

It is critical you follow our instructions because your incomplete actions can affect others' jobs as well. We are actively monitoring the software flag usages, and we will reach out to you if you miss our instructions. Failing to make corrections may result in temporary removal from the license server. We have a Grafana dashboard showing the license and software flag usages. There are software flag requests represented as "SLURM", and actual license usages as "License Server". 

License usage checking tool

If you want to make sure your license usage, you can use ~support/bin/myLicenseCheck.

  usage: ~support/bin/myLicenseCheck [-h,--help] SOFTWARE

    -h, --help      print help messages
    SOFTWARE        supported software: ansys, abaqus, comsol, schrodinger, and starccm.
  

This tool will tell you how many licenses you are actually using from the license server and how many licenses you have requested to the Slurm. But, this won't tell you about each job. So, if you want to figure out for a specific job, please make sure that the job is the only running job while you use the tool. 

For assistance

Contact OSC Help for assistance if there are any questions.

sbatch messages

shell warning

Submitting a job without specifying the proper shell will return a warning like below:

sbatch: WARNING: Job script lacks first line beginning with #! shell. Injecting '#!/bin/bash' as first line of job script.

Errors

If an error is encountered, the job is rejected.

Not specifying a project account

It is required to specify an account for a job to run. Please use the --account=<project-code> option to do this.

sbatch: error: ERROR: Job invalid: Must specify account for job
sbatch: error: Job submit/allocate failed: Unspecified error

Incorrrect resource configuration

If one makes a request for a node that doesn't exist, the job is rejected.

salloc: error: Job submit/allocate failed: Requested node configuration is not available

An example is requesting a regaular compute node, while also requesting a larger amount of memory than a compute node has.

Specify wrong account

If a user tries to set the --account option with a project that they are not on, then the job is rejected.

sbatch: error: Job submit/allocate failed: Invalid account or account/partition combination specified

Using a restricted project in a slurm job

If a user submits a job and uses a project that is restricted, the following message will be shown and the job will not be submitted:

sbatch: error: AssocGrpSubmitJobsLimit
sbatch: error: Batch job submission failed: Job violates accounting/QOS policy (job submit limit, user's size and/or time limits)

Leading whitespace in job name

Leading whitespace is not supported in SLURM job names. Your job will be rejected with an error message if you submit a job with a space in the job name:

sbatch: error: Invalid directive found in batch script: name

You can fix this by removing leading whitespace in the job name.

Script is empty or only contains whitespace

An empty file is not permitted to be submitted (included whitespace only files).

sbatch: error: Batch script is empty!

or

sbatch: error: Batch script contains only whitespace!

License problems

If you get a license error when you try to run a third-party software application, it means either the licenses are all in use or you’re not on the access list for the license. Very rarely there could be a problem with the license server. You should read the software page for the application you’re trying to use and make sure you’ve complied with all the procedures and are correctly requesting the license. Contact OSC Help with any questions.

My job is running slower than it should

Here are a few of the reasons your job may be running slowly:

• Your job has exceeded available physical memory and is swapping to disk. This is always a bad thing in an HPC environment as it can slow down your job dramatically. Either cut down on memory usage, request more memory, or spread a parallel job out over more nodes.
• Your job isn’t using all the nodes and/or cores you intended it to use. This is usually a problem with your batch script.
• Your job is spawning more threads than the number of cores you requested. Context switching involves enough overhead to slow your job.
• You are doing too much I/O to the network file servers (home and project directories), or you are doing an excessive number of small I/O operations to the parallel file server. An I/O-bound program will suffer severe slowdowns with improperly configured I/O.
• You didn’t optimize your program sufficiently.
• You got unlucky and are being hurt by someone else’s misbehaving job. As much as we try to isolate jobs from each other, sometimes a job can cause system-level problems. If you have run your job before and know that it usually runs faster, OSC staff can check for problems.

Someone deleted my job!

If your job is misbehaving, it may be necessary for OSC staff to delete it. Common problems are using up all the virtual memory on a node or performing excessive I/O to a network file server. If this happens you will be contacted by OSC Help with an explanation of the problem and suggestions for fixing it. We appreciate your cooperation in this situation because, much as we try to prevent it, one user’s jobs can interfere with the operation of the system.

Occasionally a problem not caused by your job will cause an unrecoverable situation and your job will have to be deleted. You will be contacted if this happens.

Why can’t I delete my job?

If you can’t delete your job, it usually means a node your job was running on has crashed and the job is no longer running. OSC staff will delete the job.

My job is stuck.

There are multiple reasons that your job may appear to be stuck. If a node that your job is running on crashes, your job may remain in the running job queue long after it should have finished. In this case you will be contacted by OSC and will probably have to resubmit your job.

If you conclude that your job is stuck based on what you see in the slurm output file, it’s possible that the problem is an illusion. This comment applies primarily to code you develop yourself. If you print progress information, for example, “Input complete” and “Setup complete”, the output may be buffered for efficiency, meaning it’s not written to disk immediately, so it won’t show up. To have it written immediate, you’ll have to flush the buffer; most programming languages provide a way to do this.

My job crashed. Can I recover my data?

If your job failed due to a hardware failure or system problem, it may be possible to recover your data from $TMPDIR. If the failure was due to hitting the walltime limit, the data in $TMPDIR would have been deleted immediately. Contact OSC Help for more information.

The trap command can be used in your script to save your data in case your job terminates abnormally.

Contacting OSC Help

If you are having a problem with the batch system on any of OSC's machines, you should send email to oschelp@osc.edu. Including the following information will assist HPC Client Services staff in diagnosing your problem quickly:

1. Name
2. OSC User ID (username)
3. Name of the system you are using
4. Job ID
5. Job script
6. Job output and/or error messages (preferably in context)

Or use the support request page.

Occasionally, jobs that experience problems may generate emails from staff or automated systems at the center with some information about the nature of the problem. This page provides additional information about the various emails sent, and steps that can be taken to address the problem.

batch emails

All emails from osc about jobs will come from slurm@osc.edu, oschelp@osc.edu, or an email address with the domain @osc.edu

regular job emails

These emails can be turned on/off using the appropriate slurm directives. Other email addresses can also be specified. See the mail options section of job scripts page.

other emails

There is no option to turn these emails off, as they require us to contact the user that submitted the job. We can work with you if they will be expected. Please contact OSC Help in this case.

For assistance

Contact OSC Help for assistance if there are any questions.

Overview

Slurm, which stands for Simple Linux Utility for Resource Management, is a widely used open-source HPC resource management and scheduling system that originated at Lawrence Livermore National Laboratory.

It is decided that OSC will be implementing Slurm for job scheduling and resource management, to replace the Torque resource manager and Moab scheduling system that it currently uses, over the course of 2020.

Phases of Slurm Migration

It is expected that on Jan 1, 2021, both Pitzer and Owens clusters will be using Slurm. OSC will be switching to Slurm on Pitzer with the deployment of the new Pitzer hardware in September 2020. Owens migration to Slurm will occur later this fall.

PBS Compatibility Layer

During Slurm migration, OSC enables PBS compatibility layer provided by Slurm in order to make the transition as smooth as possible. Therefore, PBS batch scripts that used to work in the previous Torque/Moab environment mostly still work in Slurm. However, we encourage you to start to convert your PBS batch scripts to Slurm scripts because

• PBS compatibility layer usually handles basic cases, and may not be able to handle some complicated cases 
• Slurm has many features that are not available in Moab/Torque, and the layer will not provide access to those features
• OSC may turn off the PBS compatibility layer in the future

Please check the following pages on how to submit a Slurm job:

• How to prepare Slurm job scripts
• How to submit, monitor and manage jobs
• Step-by-step instructions on how to submit jobs
• Slurm migration issues
• Slides for Sept 23, 2020 Workshop

Further Reading

• Slurm Documentation
• Rosetta Stone of Workload Managers

Single Account / Multiple Projects

If you work with several research groups, you had a separate account for each group. This meant multiple home directories, multiple passwords, etc. Over the years there have been requests for a single login system. We've now put that in place.

How will this affect you?

If you work with multiple groups, you'll need to be aware of how this works.

• It will be very important to use the correct project code for batch job charging.
• Managing the sharing of files between your projects (groups) is a little more complicated.
• In most cases, you will only need to fill out software license agreements once.

The single username 

We requested those with multiple accounts to choose a preferred username. If one was not selected by the user, we selected one for them. 

The preferred username will be your only active account; you will not be able to log in or submit jobs with the other accounts. 

Checking the groups of a username

To check all groups of a username (USERID), use the command:

groups USERID

or

OSCfinger USERID

The first one from the output is your primary group, which is the project code (PROJECTID) this username (USERID) was created under.

All project codes your user account is under is determined by the groups displayed. One can also use the OSC Client Portal to look at their current projects.

Changing the primary group for a login session

You can change the primary group of your username (USERID) to any UNIX group (GROUP) that username (USERID) belongs to during the login session using the command:

newgrp GROUP

This change is only valid during this login session. If you log out and log back in, your primary group is changed back to the default one.

Check previous user accounts

There is no available tool to check all of your previous active accounts. We sent an email to each impacted user providing the information on your preferred username and previous accounts. Please refer to that email (sent on July 11, subject "Multiple OSC Accounts - Your Single Username").

Batch job

How to specify the charging project

Specify a project to charge the job to using the -A flag. e.g. The following example will charge to project PAS1234.

#SBATCH -A PAS1234

Batch limits policy

The job limit per user remains the same. That is to say, though your jobs are charged against different project codes, the total number of jobs and cores your user account can use on each system is still restricted by the previous user-based limit. Therefore, consolidating multiple user accounts into one preferred user account may affect the work of some users.

Please check our batch limit policy on each system for more details.

Data Management

Managing multiple home directories

Data from your non-preferred accounts will remain in those home directories; the ownership of the files will be updated to your preferred username, the newly consolidated account. You can access your other home directories using the command cd /absolute/path/to/file

You will need to consolidate all files to your preferred username as soon as possible because we plan to purge the data in future. Please contact OSC Help if you need the information on your other home directories to access the files.  

Previous files associated with your other usernames

• Files associated with your non-preferred accounts will have their ownership changed to your preferred username. 
• These files won't count against your home directory file quota. 
• There will be no change to files and quotas on the project and scratch file systems.

Change group of a file

Log in with preferred username (P_ USERID) and create a new file of which the owner and group is your preferred username (P_ USERID) and primary project code (P_PROJECTID). Then change the group of the newly created file (FILE) using the command:

chgrp PROJECTID FILE

Managing file sharing in a batch job

In the Linux file system, every file has an owner and a group. By default, the group (project code) assigned to a file is the primary group of the user who creates it. This means that even if you change the charged account for a batch job, any files created will still be associated with your primary group.

To change the group for new files you will need to update your primary group prior to submitting your slurm script using the newgrp command.

It is important to remember that groups are used in two different ways: for resource use charging and file permissions. In the simplest case, if you are a member of only one research group/project, you won't need either option above. If you are in multiple research groups and/or multiple projects, you may need something like:

newgrp PAS0002
sbatch -A PAS0002 myjob.sh

OnDemand users

If you use the OnDemand Files app to upload files to the OSC filesystem, the group ownership of uploaded files will be your primary group.

Software licenses

• We will merge all your current agreements if you have multiple accounts.  
• In many cases, you will only need to fill out software license agreements once.
• Some vendors may require you to sign an updated agreement.  
• Some vendors may also require the PI of each of your research groups/project codes to sign an agreement.

Problem Description

Our current GPFS file system is a distributed process with significant interactions between the clients. As the compute nodes being GPFS flle system clients, a certain amount of memory of each node needs to be reserved for these interactions. As a result, the maximum physical memory of each node allowed to be used by users' jobs is reduced, in order to keep the healthy performance of the file system. In addition, using swap memory is not allowed.  

The table below summarizes the maximum physical memory allowed for each type of nodes on our systems:

Owens Cluster

Pitzer Cluster

Solutions When You Need Regular Nodes

If you do not request memory explicitly in your job (no --mem ) 

Your job can be submitted and scheduled as before, and resources will be allocated according to your requests for cores/nodes ( --nodes=XX --ntask=XX ).  If you request a partial node, the memory allocated to your job is proportional to the number of cores requested; if you request the whole node, the memory allocated to your job is based on the information summarized in the above tables.

If you have a multi-node job (  nodes>1  ), your job will be assigned the entire nodes with maximum memory allowed per node and charged for the entire nodes regardless of --ntask request.

If you do request memory explicitly in your job (with  --mem  ) 

If you request memory explicitly in your script, please re-visit your script according to the following pages:

Pitzer: https://www.osc.edu/resources/technical_support/supercomputers/pitzer/batch_limit_rules 

Owens: https://www.osc.edu/resources/technical_support/supercomputers/owens/batch_limit_rules 

Pitzer Compilers

The Skylake processors that make up the original Pitzer cluster and the Cascade Lake processors in its expansion support the AVX512 instruction set, but you must set the correct compiler flags to take advantage of it. AVX512 has the potential to speed up your code by a factor of 8 or more, depending on the compiler and options you would otherwise use.

With the Intel compilers, use -xHost and -O2 or higher. With the gnu compilers, use -march=native and -O3. The PGI compilers by default use the highest available instruction set, so no additional flags are necessary.

This advice assumes that you are building and running your code on Pitzer. The executables will not be portable.  Of course, any highly optimized builds, such as those employing the options above, should be thoroughly validated for correctness.

Owens Compilers

The Haswell and Broadwell processors that make up Owens support the Advanced Vector Extensions (AVX2) instruction set, but you must set the correct compiler flags to take advantage of it. AVX2 has the potential to speed up your code by a factor of 4 or more, depending on the compiler and options you would otherwise use.

With the Intel compilers, use -xHost and -O2 or higher. With the gnu compilers, use -march=native and -O3. The PGI compilers by default use the highest available instruction set, so no additional flags are necessary.

This advice assumes that you are building and running your code on Owens. The executables will not be portable. Of course, any highly optimized builds, such as those employing the options above, should be thoroughly validated for correctness.

Further Reading:

Intel Compiler Page

PGI Compiler Page

GNU Complier Page

Connections to OSC

In order for users to access OSC resources through the web your firewall rules should allow for connections to the following publicly-facing IP ranges.  Otherwise, users may be blocked or denied access to our services.

• 192.148.248.0/24
• 192.148.247.0/24
• 192.157.5.0/25

The followingg TCP ports should be opened:

• 80 (HTTP)
• 443 (HTTPS)
• 22 (SSH)

The following domain should be allowed:

• *.osc.edu

Users may follow the instructions below "Test your configuration" to ensure that your system is not blocked from accessing our services. If you are still unsure of whether their network is blocking theses hosts or ports should contact their local IT administrator.

Test your configuration

[Windows] Test your connection using PuTTY

1. Open the PuTTY application.
2. Enter IP address listed in "Connections to OSC" in the "Host Name" field.
3. Enter 22 in the "Port" field.
4. Click the 'Telnet' radio button under "Connection Type".
5. Click "Open" to test the connection.
6. Confirm the response. If the connection is successful, you will see a message that says "SSH-2.0-OpenSSH_5.3", as shown below. If you receive a PuTTY error, consult your system administrator for network access troubleshooting.

[OSX/Linux] Test your configuration using telnet

1. Open a terminal.
2. Type telnet IPaddress 22 (Here, IPaddress is IP address listed in "Connections to OSC").
3. Confirm the connection. 

Connections from OSC

All outbound network traffic from all of OSC's compute nodes are routed through a network address translation host (NAT) including the following IPs:

• 192.148.249.248
• 192.148.249.249
• 192.148.249.250
• 192.148.249.251

IT and Network Administrators

Please use the above information in order to assit users in acessing our resources.  

Occasionally new services may be stood up using hosts and ports not described here.  If you believe our list needs correcting please let us know at oschelp@osc.edu.

Job charging based on usage

Jobs are charged based length, number of cores, amount of memory, single node versus multi-node, and type of resource.

Length and number of cores

Jobs are recorded in terms of core-hours hours used. Core-hours can be calculated by:

number of cores * length of job

e.g.

A 4 core job that runs for 2 hours would have a total core-hour usage of:

4 cores * 2 hours = 8 core-hours

Amount of Memory

Each processor has a default amount of memory paired along with it, which differs by cluster. When requesting a specifc amount of memory that doesn't correlate with the default pairing, the charging uses an algorithm to determine if the effective cores should be used.

The value for effective cores will be used in place of the actual cores used if and only if it is larger than the explicit number of cores requested.

effective cores = memory / memory per core

e.g.

A job that requests  nodes=1:ppn=3  will still be charged for 3 cores of usage.

However, a job that requests  nodes=1:ppn=1,mem=12GB, where the default memory allocated per core is 4GB, then the job will be charged for 3 cores worth of usage.

effective cores = 12GB / (4GB/core) = 3 core

Single versus Multi-Node

If requesting a single node, then a job is charged for only the cores/processors requested. However, when requesting multiple nodes the job is charged for each entire node regardless of the number of cores/processors requested.

Type of resource

Depending on the type of node requested, it can change the dollar rate charged per core-hour. There are currently three types of nodes, regular, hugememory,and gpu.

If a gpu node is used, there are two metrics recorded, core-hours and gpu-hours. Each has a different dollar-rate, and these are combined to determine the total charges for usage.

e.g.

A job requests nodes=1:ppn=8:gpus=2 and runs for 1 hour.

The usage charge would be calculated using:

8 cores * 1 hour = 8 core-hours

and

2 gpus * 1 hour = 2 gpu-hours

and combined for:

8 core-hours + 2 gpu-hours

Project storage charging based on quota

Projects that request extra storage be added are charged for that storage based on the total space reserved (i.e. your quota). 

The rates are in TB per month:

storage quota in TB * rate per month

Problem description

A common problem on our systems is that a user's job causes a node out of memory or uses more than its allocated memory if the node is shared with other jobs.

If a job exhausts both the physical memory and the swap space on a node, it causes the node to crash. With a parallel job, there may be many nodes that crash. When a node crashes, the OSC staff has to manually reboot and clean up the node. If other jobs were running on the same node, the users have to be notified that their jobs failed.

If your job requests less than a full node, for example, --ntasks-per-node=4, it may be scheduled on a node with other running jobs. In this case, your job is entitled to a memory allocation proportional to the number of cores requested. For example, if a system has 4.5 GB per core and you request one core, it is your responsibility to make sure your job uses no more than 4.5 GB. Otherwise your job will interfere with the execution of other jobs.

Example errors

# OOM in a parallel program launched through srun

slurmstepd: error: Detected 1 oom-kill event(s) in StepId=14604003.0 cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.

srun: error: o0616: task 0: Out Of Memory

# OOM in program run directly by the batch script of a job

slurmstepd: error: Detected 1 oom-kill event(s) in StepId=14604003.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.

Background

Each node has a fixed amount of physical memory and a fixed amount of disk space designated as swap space. If your program and data don’t fit in physical memory, the virtual memory system writes pages from physical memory to disk as necessary and reads in the pages it needs. This is called swapping. 

You can find the amount of usable memory on our system at default memory limits. You can see the memory and swap values for a node by running the Linux command free on the node.

In the world of high-performance computing, swapping is almost always undesirable. If your program does a lot of swapping, it will spend most of its time doing disk I/O and won’t get much computation done. Swapping is not supported at OSC. Please consider the suggestions below.

Suggested solutions

Here are some suggestions for fixing jobs that use too much memory. Feel free to contact OSC Help for assistance with any of these options.

Some of these remedies involve requesting more processors (cores) for your job. As a general rule, we require you to request a number of processors proportional to the amount of memory you require. You need to think in terms of using some fraction of a node rather than treating processors and memory separately. If some of the processors remain idle, that’s not a problem. Memory is just as valuable a resource as processors.

Request whole node or more processors

Jobs requesting less than a whole node are those that request less than the total number of available cores. These jobs can be problematic for two reasons. First, they are entitled to use an amount of memory proportional to the cores requested; if they use more they interfere with other jobs. Second, if they cause a node to crash, it typically affects multiple jobs and multiple users.

If you’re sure about your memory usage, it’s fine to request just the number of processors you need, as long as it’s enough to cover the amount of memory you need. If you’re not sure, play it safe and request all the processors on the node.

Reduce memory usage

Consider whether your job’s memory usage is reasonable in light of the work it’s doing. The code itself typically doesn’t require much memory, so you need to look mostly at the data size.

If you’re developing the code yourself, look for memory leaks. In MATLAB look for large arrays that can be cleared.

An out-of-core algorithm will typically use disk more efficiently than an in-memory algorithm that relies on swapping. Some third-party software gives you a choice of algorithms or allows you to set a limit on the memory the algorithm will use.

Use more nodes for a parallel job

If you have a parallel job you can get more total memory by requesting more nodes. Depending on the characteristics of your code you may also need to run fewer processes per node.

Here’s an example. Suppose your job on Pitzer includes the following lines:

#SBATCH --nodes=2
#SBATCH --ntasks-per-node=48
…
mpiexec mycode

This job has 2 nodes worth of memory available to it (specifically 178GB * 2 nodes of memory). The mpiexec command by default runs one process per core, which in this case is 96 copies of mycode.

If this job uses too much memory you can spread those 96 processes over more nodes. The following lines request 4 nodes, giving you a total of 712 GB of memory (4 nodes *178 GB). The -ppn 24 option on the mpiexec command says to run 24 processes per node instead of 48, for a total of 96 as before.

#SBATCH --nodes=4
#SBATCH --ntasks-per-node=48
…
mpiexec -ppn 24 mycode

Since parallel jobs are always assigned whole nodes, the following lines will also run 24 processes per node on 4 nodes.

#SBATCH --nodes=4
#SBATCH --ntasks-per-node=24
…
mpiexec mycode

Request large-memory nodes

Pitzer has 4 huge memory nodes with ~3 TB of memory and with 80 cores. Owens has 16 huge memory nodes with ~1.5 TB of memory and with 48 cores.

Since there are so few of these nodes, compared to hundreds of standard nodes, jobs requesting them will often have a long wait in the queue. The wait will be worthwhile, though, if these nodes solve your memory problem. See the batch limit pages for Owens and Pitzer to learn how to request huge or large memory nodes.

How to monitor your memory usage

Grafana

If a job is currently running, or you know the timeframe that it was running, then grafana can be used to look at the individual nodes memory usage for jobs. Look for the graph that shows memory usage.

OnDemand

You can also view node status graphically using the OSC OnDemand Portal. Under "Jobs" select "Active Jobs." Click on "Job Status" and scroll down to see memory usage.

XDMoD

To view detailed metrics about jobs after waiting a day after the jobs are completed, you can use the XDMoD tool. It can show the memory usage for jobs over time as well as other metrics. Please see the job view how-to for more information on looking jobs.

sstat

Slurm command sstat can be used to obtain info for running jobs.

sstat --format=AveRSS,JobID -j <job-id> -a

During job

Query the job's cgroup which is what controls the amount of memory a job can use:

# return current memory usage
cat /sys/fs/cgroup/memory/slurm/uid_$(id -u)/job_$SLURM_JOB_ID/memory.usage_in_bytes | numfmt --to iec-i
# return memory limit
cat /sys/fs/cgroup/memory/slurm/uid_$(id -u)/job_$SLURM_JOB_ID/memory.limit_in_bytes | numfmt --to iec-i

Notes

If it appears that your job is close to crashing a node, we may preemptively delete the job.

If your job is interfering with other jobs by using more memory than it should be, we may delete the job.

In extreme cases OSC staff may restrict your ability to submit jobs. If you crash a large number of nodes or continue to submit problematic jobs after we have notified you of the situation, this may be the only way to protect the system and our other users. If this happens, we will restore your privileges as soon as you demonstrate that you have resolved the problem.

For details on retrieving files from unexpectedly terminated jobs see this FAQ.

For assistance

OSC has staff available to help you resolve your memory issues. See our client support request page for contact information.

XDMoD Overview

XDMoD, which stands for XD Metrics on Demand, is an NSF-funded open source tool that provides a wide range of metrics pertaining to resource utilization and performance of high-performance computing (HPC) resources, and the impact these resources have in terms of scholarship and research.

How to log in

Visit OSC's XDMoD (xdmod.osc.edu) and click 'Sign In' in the upper left corner of the page.

XDMoD Tabs

When you first log in you will be directed to the Summary tab. The different XDMoD tabs are located near the top of the page. You will be able to change tabs simply by click on the one you would like to view. By default, you will see the data from the previous month, but you can change the start and end date and then click 'refresh' to update the timeframe being reported.

Summary:

The Summary tab is comprised of a duration selector toolbar, a summary information bar, followed by a select set of charts representative of the usage. The Summary tab provides a dashboard that presents summary statistics and selected charts that are useful to the role of the current user. More information can be found at the XDMoD User Manual. 

Usage:

The Usage tab is comprised of a chart selection tree on the left, and a chart viewer to the right of the page. The usage tab provides a convenient way to browse all the realms present in XDMoD. More information can be found at the XDMoD User Manual. 

Metric Explorer:

The Metric Explorer allows one to create complex plots containing multiple multiple metrics. It has many points and click features that allow the user to easily add, filter, and modify the data and the format in which it is presented. More information can be found at the XDMoD User Manual. 

App Kernels:

The Application Kernels tab consists of three sub-tabs, and each has a specific goal in order to make viewing application kernels simple and intuitive. The three sub-tabs consist of the Application Kernels Viewer, Application Kernels Explorer, and the Reports subsidiary tabs. More information can be found at the XDMoD User Manual. 

Report Generator:

This tab will allow you to manage reports. The left region provides a listing of any reports you have created. The right region displays any charts you have chosen to make available for building a report. More information can be found at the XDMoD User Manual. 

Job Viewer:

The Job Viewer tab displays information about individual HPC jobs and includes a search interface that allows jobs to be selected based on a wide range of filters. This tab also contains the SUPReMM module. More information on the SUPReMM module can be found below in this documentation. More information can be found at the XDMoD User Manual. 

About:

This tab will display information about XDMoD.

Different Roles

XDMoD utilizes roles to restrict access to data and elements of the user interface such as tabs. OSC client holds the 'User Role' by default after you log into OSC XDMoD using your OSC credentials. With 'User Role', users are able to view all data available to their personal utilization information. They are also able to view information regarding their allocations, quality of service data via the Application Kernel Explorer, and generate custom reports. We also support the 'Principal Investigator' role, who has access to all data available to a user, as well as detailed information for any users included on their allocations or project.

References, Resources, and Documentation